Russ99ej7

Hey everyone, this is my first post and have been trying to figure out what's wrong with my car and have had zero luck. My car was experiencing random/intermittent misfires when not under load and would go away when under acceleration. At times when not under load/maintained speed the misfires would come and go.

I had a p0300 dtc as well as misfires on cylinders 1 - 4. I did the usual, new cap & rotor, then put two different sets of wires on it, as well as new plugs. I recently got a newer dizzy for it and it seems to not have corrected the problem at all. My car is a 99 civic HX. When purchasing a dizzy for it, the parts guy gave me the wrong dizzy at first, but apparently my car has the 98 wiring harness on it. My motor is a D16Y5 Vtec-E. I've thrown a few parts at it, and seems to have gotten worse and the sound appears that the Vtec is engaging at later RPM than it should be. D16Y5 vtec should engage around 2,700 RPMs and sounds like it's engaging at 4,700 instead, but not confirmed if that is indeed what is happening.

The following is a list of parts that I've thrown at it to no success, just to eliminate what could be wrong with it:
New Plugs (gapped at .043")
New dizzy
New Vtec Solenoid
EGR Valve

I installed a new exhaust header which removed the cat and only could install one of the two o2 sensors and have the 2nd o2 sensor cable tied off to the side. (Problem was occurring before this mod)
I also had an alternator problem involving a loose bracket <--only discovered when I went to install a new alternator. Not sure if the poor connecting for the alternator caused some voltage variance and screwed up the computer.
Any help would be great, as a friend of mine works at Honda and is mildly puzzled at this and is of no help.